I wouldn't call it a "major cliffhanger"; more of a Gekko Ending. Really about the only things not covered in the game is Trigger being on the moon (but between Roll and Tron working on the problem that's pretty much practically resolved) and the reactivation of the Master System. But really that's no more a cliffhanger than ending a normal Megaman game by saying "And Wily escaped...again." Just means that if there's another game you'll be fighting another set of themed bosses.
Don't get me wrong; I love MML. But there was nothing really cliffhangery about the ending like some fans seem to make it out to be.
Wow, thats it? That is certainly underwhelming.
Honestly if you wanted to dig into it a bit you could come up with a rather lengthy list of unresolved questions unanswered between the two games. Like what exactly "is" the Elder system, what'll happen with the developed relationships between characters, standard stuff like that. Back when MML2 came out it probably actually did qualify as a rather decent cliffhanger; however seeing as how lazy the Japanese gaming and anime writing has become these days it's really no more of a cliffhanger than most of the stuff they crap out and either just fail to follow up on or the budget ran out.
Let me try think of a point of comparison...okay; got it (I think). Imagine if the Phoenix Wright series had ended at Justice For All instead of Trials and Tribulations. (Not the over all story mind you, just Phoenix's arc.) There might've been a decent list of questions about "what if" and "well what about what happened at X time period" and so on; but there wasn't exactly any dangling plot threads aside from (just in case)
DeKiller getting away and never being caught.
Having a sequel wasn't exactly because the story "needed" it but rather there was still plenty of good story to be told and characters to develop. I look at MML3 in the same light.